model-calibration-species"
In atlantistools: Process and Visualise Output from Atlantis Models

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NOTE: This vigentte is optimised for longer simulation runs. Therefore the output is not as pleasant due to the fact that the dummy setas file have a simulation time of 5 years.

In order to use this vignette make sure to render model-preprocess.Rmd first. Either save the resulting list of dataframes as shown in data-raw/data-vignette-model-preprocess.R or render both vignettes model-preprocess.Rmd and model-calibration-species.Rmd in the same R-instance. Of course, you can also use a personalised version of mode-preprocess.Rmd. Please make sure to add all resulting dataframes to the list of dataframes at the end of the preprocess vignette and change model-calibration-species.Rmd accordingly.

library("atlantistools")
library("gridExtra")

# You should be able to build the vignette either by clicking on "Knit PDF" in RStudio or with
# rmarkdown::render("model-calibration-species.Rmd")

User Input

This section is used to read in the SETAS dummy files. Please change this accordingly.

result <- preprocess
species <- c("Shallow piscivorous fish", "Small planktivorous fish")

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Overview species

plots <- lapply(species, plot_species, data_pre = result)
for (i in seq_along(plots)) {
  cat(paste0("## ", species[i]), sep = "\n")
  gridExtra::grid.arrange(plots[[i]])
  cat("\n\n")
}